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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9069@e493248
This commit is contained in:
github-actions
@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9068</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9069</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -200,10 +200,10 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="va">x</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1 128 0.025 0.002 2 8 0.025 2 128 0.5 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.005 256 0.5 128 32 32 128 128 0.5 0.025</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.03073988 1.36755493 -0.98560777 -1.68148803 0.22171346 0.60366062</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.98560777 0.22171346 1.36755493 -0.16023370</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.7639563 0.9825666 -0.5975237 0.8070010 0.4558698 0.4558698</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8070010 0.8070010 -0.5975237 -1.3563056</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">y</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
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<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
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@ -213,38 +213,38 @@
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<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="va">y</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 4 >=4 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 16 >=4 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.5 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 >=4 4 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 0.125 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.25 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 <=0.0625 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 64 0.5 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 32 2 4 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J <=2 0.5 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A >=64 4 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 2 0.5 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=4 2 >=4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=4 <=0.125 1 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 1 0.25 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 <=0.125 >=4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G >=64 0.5 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.25 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I <=4 <=0.125 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=64 0.25 2 1</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
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<span class="r-msg co"><span class="r-pr">#></span> "id" and "tobr"</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.08036866 0.51076165 -0.04318986 0.15636345 -0.75415022 0.48217462</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.97945442 0.75675773 0.20085706 -0.24975135</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.57566233 -0.17235135 0.62175861 -0.97114505 -0.17254362 0.15946520</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.05465037 -0.07283047 -0.09101057 0.17764530</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 <=0.0625 1 2 -0.97945442</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 0.125 1 1 -0.75415022</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J <=2 0.5 4 2 -0.24975135</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 4 >=4 1 4 -0.08036866</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.5 2 2 -0.04318986</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 >=4 4 <=0.5 0.15636345</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 32 2 4 <=0.5 0.20085706</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.25 4 4 0.48217462</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 16 >=4 2 4 0.51076165</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 64 0.5 4 4 0.75675773</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=4 <=0.125 1 <=0.5 -0.97114505</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 1 0.25 2 -0.17254362</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 2 0.5 <=0.5 -0.17235135</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I <=4 <=0.125 2 4 -0.09101057</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.25 1 2 -0.07283047</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G >=64 0.5 0.5 1 -0.05465037</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 <=0.125 >=4 2 0.15946520</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=64 0.25 2 1 0.17764530</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A >=64 4 0.5 2 0.57566233</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=4 2 >=4 4 0.62175861</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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@ -256,17 +256,17 @@
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C 16 0.5 2 2 -0.04318986 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 A 4 >=4 1 4 -0.08036866 0.0371788</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 D 16 >=4 4 <=0.5 0.15636345 0.1995533</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J <=2 0.5 4 2 -0.24975135 0.2065615</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I 32 2 4 <=0.5 0.20085706 0.2440469</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.25 4 4 0.48217462 0.5253645</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B 16 >=4 2 4 0.51076165 0.5539515</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 E 16 0.125 1 1 -0.75415022 0.7109604</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 H 64 0.5 4 4 0.75675773 0.7999476</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G 4 <=0.0625 1 2 -0.97945442 0.9362646</span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C <=4 2 >=4 4 0.62175861 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 A >=64 4 0.5 2 0.57566233 0.04609628</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J >=64 0.25 2 1 0.17764530 0.44411330</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F 16 <=0.125 >=4 2 0.15946520 0.46229341</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 G >=64 0.5 0.5 1 -0.05465037 0.67640897</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H 16 0.25 1 2 -0.07283047 0.69458908</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 I <=4 <=0.125 2 4 -0.09101057 0.71276918</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B 32 2 0.5 <=0.5 -0.17235135 0.79410996</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E 16 1 0.25 2 -0.17254362 0.79430223</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D <=4 <=0.125 1 <=0.5 -0.97114505 1.59290366</span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
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<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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